That is all easy stuff no need to pull the engine, There is plenty of room under the hood of a YJ. Especially a 4 banger Hell you could probably sit in the engine bay and do all of that

+1

Some thoughts on the motor mounts:
The driver's motor mount is super easy. The passenger is pretty difficult. To remove the motor mount bolt, you can either remove the alternator or remove the mount bracket from the engine. I did the mount bracket, but it's difficult and must be mostly done from under the car. I'll recommend removing the alternator. Consider doing a 1" motor mount lift and 1" body lift at the same time, if you need more tire or ground clearance.

The transmission mount is also super easy.

The broken exhaust bolts may require the head to be removed. I would just remove the head, not the entire engine. The broken bolts sound like the most difficult part.

I don't recommend Brown Dog motor mounts for 2.5L engines - I would stick with the stock mounts. I have the Brown Dog with my 2.5L, and they greatly increase the vibes. They seem to be fine with the 4.0L engines, and the Brown Dog mounts are very well-made.

The 1" motor mount lift would probably also allow you to remove the transfer case drop that you installed. I'm personally not a fan of transfer case drops.

You will need a body lift kit if you want to use a motor mount lift. I used a Daystar 1" Body Lift Kit.

The 1" motor mount spacer blocks range from $55 to $75. Rough Country 1" Motor Mount Blocks I don't recommend Brown Dog motor mounts for 2.5L engines - I would stick with the stock mounts. I have the Brown Dog with my 2.5L, and they greatly increase the vibes. They seem to be fine with the 4.0L engines, and the Brown Dog mounts are very well-made. The 1" motor mount lift would probably also allow you to remove the transfer case drop that you installed. I'm personally not a fan of transfer case drops. You will need a body lift kit if you want to use a motor mount lift. I used a Daystar 1" Body Lift Kit.

Where are you Getting your info from some things you are wrong about 1. You do NOT need a bl for a 1" Mml. 2. The poly mounts With the brown dogs are bad with the 2.5 the rubber are not bad at all ( I've run both on a 2.5) 3. RC really they can't even make a spring the proper length you would trust their junk holding your engine

You can replace both motor mounts without removing anything at all. New mounts stock or Brown Dog in good old rubber.

When tightening the long motor mount bolts be sure to torque to spec. If you over tighten you will pull the ears of the mount to contact the rubber center sleeve and have bad vibes.

The exhaust manifold gasket should be done in conjunction with drivers side motor mount. Usually the exhaust manifold on the 2.5L is not cracked but check to make sure. Get a good Felpro gasket one single piece crush gasket.

The broken studs suck but can be done with the head still installed. Or take it to a machinist and watch. If you don't have any experience you may need the machinist or remove the head to have it done for you.

Where are you Getting your info from some things you are wrong about 1. You do NOT need a bl for a 1" Mml. 2. The poly mounts With the brown dogs are bad with the 2.5 the rubber are not bad at all ( I've run both on a 2.5) 3. RC really they can't even make a spring the proper length you would trust their junk holding your engine

Wow...pretty strong words on a friendly forum. You having a bad day?

1) you'll have interference if you don't do a body lift. Definitely at the radiator shroud. Maybe other places. I shared my experience, and I'd recommend the BL and MML together. It's great that you shared your viewpoint with the OP too.

2) I've used both the poly and soft rubber Brown Dog mounts with my 2.5l, and torqued the bolts properly. The vibes are much worse than stock on my Jeep. If you had a different experience, then great!

3) The RC motor mount lift is a block of aluminum. Unless you have first hand experience with the mount, then you are not really adding anything helpful. I used the Brown Dog 1" mount, so I don't have any first hand experience. I was just sharing an inexpensive option for the OP.

Wow...pretty strong words on a friendly forum. You having a bad day? 1) you'll have interference if you don't do a body lift. Definitely at the radiator shroud. Maybe other places. I shared my experience, and I'd recommend the BL and MML together. It's great that you shared your viewpoint with the OP too. 2) I've used both the poly and soft rubber Brown Dog mounts with my 2.5l, and torqued the bolts properly. The vibes are much worse than stock on my Jeep. If you had a different experience, then great! 3) The RC motor mount lift is a block of aluminum. Unless you have first hand experience with the mount, then you are not really adding anything helpful. I used the Brown Dog 1" mount, so I don't have any first hand experience. I was just sharing an inexpensive option for the OP.

I've run the Browndog MML on my 95 before I installed my BL I never had any interference issues at all. If the fan is close to the shroud it takes a few seconds to trim it with a razor.

Both motor mounts & trans mount went in without a hitch, I used stock style mounts from from Rock Auto because the jeep is getting fixed up for my girls son "Reid" that is coming back home from Serving 2 years Over seas out of his 5 years in the Marines ( He's a Cop )

The broken Front & rear exhaust bolts came out using a reverse drill bit.

Intake & exhaust manifold gasket was easy.

still have to do Valve cover gasket.

Fix whatever brakes while doing the above stuff. well I found that the bad motor mounts had twisted enough to crack the exhaust manifold so i ordered one from Rock Auto, it bolted right-up and working fine. I like the fact that it has a O2 sensor bung in the cast manifold instead of down stream in the exhaust tubing.

I used stock style replacements because after Reid is done using the jeep I plan on putting a LS 5.7 liter with a overdrive auto in it with 35" tires.